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Thursday, July 14, 2016

Beer Made With 45 Million Year Old Yeast?

The other day I came across a Reddit post entitled: “Beer
Made With 45 Million-Year-Old Yeast Found in Amber.”

And I was intrigued.

The link led to an Indiegogo campaign from the Fossil Fuels
Brewing Co. aiming to raise money to further their production of beer made
with ancient yeast. As the story goes, the idea was born after the “chance
discovery of a beautiful amber stone, replete with a 45 million year old leaf,
and a single yeast spore – still alive and itching to make beer.”

Immediately, I thought, This sounds like BS. I distinctly recall recent studies showing DNA doesn't last that long, especially in amber. Thousands of years? Sure. But 45 million? No way cells live that long.

But mid-scoff, I noticed two of the brewery team-members are published
microbiologists, one of whom – Dr. Raul Cano – is allegedly the “first
scientist to isolate viable DNA from an amber crystal.” Plus I remembered
recently coming across a paper in Nature(!)
claiming to have revived 250-million-year-old bacteria. Perhaps my initial reaction was wrong.

My skeptic senses were tingling, but my scientist's trusty maybe-I'm-mistaken alarm was buzzing as well. So I did some investigating.

Here's what I found.

Long-slumbering spores

Dr. Cano did indeed make headlines for a 1995 Science paper describing the discovery of
dormant, still-living bacterial spores from the gut of a fossil bee preserved
in 25- to 40-million-year-old Dominican amber. He and his co-author even claimed to have revived and cultured these microbes, which were similar to modern Bacillus bacteria. They explained the
measures they took to confirm these bacteria weren’t lab contaminants, but in
fact ancient, tens-of-millions-of-years-old prehistoric survivors.

Amber from the Dominican is famous for containing ancient insects.
This is a bee, not unlike the bee in whose gut Dr. Cano supposedly
discovered spores.
Image by Michael S. Engel via Wikipedia.

This wasn’t the only such report. Actually, the 90s to early
2000s were somewhat of a heyday for super-ancient DNA and microbes. Cano and
other researchers published several reports of DNA extracted from bones,
plants, and insects at tens or even hundreds of millions of years old, plus the
resurrection of other ancient bacteria, including Staphylococcus
from Dominican amber and Micrococcus from
Israeli amber as old as 120 million years.

(Interestingly, it doesn’t look like Dr. Cano has ever
published on the yeast supposedly used for this beer.)

The study that took the cake, however, was the October 2000 report I mentioned
earlier, of Bacillus bacteria preserved not in amber, but in a salt crystal 250 million years old. If true,
those individual cells would be older than the first dinosaurs. Some researchers
also pointed out the noteworthy implications for inter-planetary transport of dormant
microbes. The age of ancient DNA and fossil microbe resurrection seemed upon
us.

Problem was, well, there were problems.

Problems

As you’d expect, these studies inspired some controversy. As
they say, extraordinary claims require extraordinary evidence, and not everyone
was convinced the evidence was sufficient. For starters, scientific understanding indicated that DNA shouldn't last that long in fossils. Critics also pointed
out that many of these supposedly ancient DNA sequences were suspiciously similar to the sort of modern-day species you'd expect to find as lab contaminants. Understandably, many researchers questioned the procedures used in these extraordinary discoveries.

But of all the issues, perhaps the biggest was reproducibility. It is generally accepted that DNA, and even spores, can survive in fossils thousands of years old, but only after numerous repeated experiments removed all doubt. But no such repetition was presented for these millions-of-years-old examples. A number of other scientists in other labs
tried to extract DNA from their own ancient amber samples, and repeatedly
failed. On top of that, it seems the original researchers were unable to replicate their
own experiments.

In order to rule out the possibility that lab contamination was responsible for these supposedly ancient samples, researchers would be expected to replicate their extractions in separate laboratories. Finding the same result in two labs would be a big clue that this was no mistake. But as a 2005 critique stated: “Intriguingly, no claims of
geologically ancient cultures or DNA sequences published to date (i.e., claims
>1 [million years]) have followed this simple criterion of authentication.”

Extracting DNA and microbes from fossils is a very delicate process.
As you can imagine, contamination by modern microbes is VERY likely,
so careful procedures are followed to avoid it.
Image from University of Copenhagen.

For those reasons, these claims remained controversial and unproven for several years. And then a few years ago two more important studies came out. I've already alluded to them at the beginning of this post; they were the first studies that came to my
mind when I read that dubious headline.

In 2012, a team of scientists put their minds to answering the
question: Just how long does DNA last in fossils anyway? They studied DNA preserved in
a series of fossils of different ages, and used the data to estimate the rate of DNA decay. Even under ideal conditions, their calculations indicate that DNA would degrade into illegibility in perhaps 1.5 million years, a far cry from 250,
120, or even 45 million.

And in 2013, the question of DNA survivability in amber was
answered dramatically. Researchers attempted to extract DNA from insects trapped in two specimens
of copal (that is, partially-fossilized tree resin before it becomes amber), one dated to around 10,600 years
old, the other younger than 60 years old. And they found no ancient DNA. In either sample. Turns out amber is really really
bad at preserving DNA.

These two studies supported the implications of earlier findings: DNA simply does not last very long in fossils. And with no known mechanism for cells to preserve their own DNA for millions of years, these results cast some serious doubt on these ancient microbes.

So, 45 Million Year-Old Yeast?

In science, it's always hard to justify a definitive 'no.' But, no.

To date, claims of living microbes from fossils millions of years old are plagued with uncertainty, and none have been replicated, including apparently Dr. Cano's own bacteria and yeast. What's more, studies have repeatedly shown that millions of years is too long for the survival of DNA, let alone living cells. Especially in amber.

Apparently critics say this beer is unusual but tasty. I'm certainly in no position to dispute that claim. But more than likely that yeast came from someone's hands or clothes, not from the Eocene.